Major shifts in gut microbiota during development and its relationship to growth in ostriches

The development of gut microbiota during ontogeny in vertebrates is emerging as an important process influencing physiology, immunity, and fitness. However, there is little knowledge of how bacteria colonise the juvenile gut, how this is influenced by changes in the diversity of gut bacteria, and to what extent this influences host fitness, particularly in non-model organisms. Here, we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiota in ostriches (Struthio camelus; n = 71) over the first three months of life, during which time there was a five-fold difference in growth. We found a gradual increase in microbial diversity with age that involved multiple colonisation and extinction events and a major taxonomic shift in bacteria that coincided with the cessation of yolk absorption. Growth immediately after hatching was strongly positively correlated with the abundance of Bacteroides and negatively correlated with Akkermansia. After the first week of age, the abundances of six phylogenetically diverse families (Peptococcaceae, S24-7, Verrucomicrobiae, Anaeroplasmataceae, Streptococcaceae, Methanobacteriaceae) were associated with subsequent reductions in chick growth in an age-specific and transient manner. These results have broad implications for our understanding of the development of gut microbiota and its associations with animal growth.